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  • Jan 31 2019 22:37

    bebatut on gh-pages

    Update on: Thu Jan 31 22:36:58 … (compare)

  • Jan 31 2019 22:00

    erasche on master

    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

  • Jan 31 2019 22:00
    erasche closed #1237
  • Jan 31 2019 22:00
    erasche commented #1237
  • Jan 31 2019 21:33
    jmchilton synchronize #1237
  • Jan 31 2019 21:01
    erasche labeled #1239
  • Jan 31 2019 21:01
    erasche opened #1239
  • Jan 31 2019 21:00
    natefoo opened #1238
  • Jan 31 2019 20:56
    jmchilton opened #1237
  • Jan 31 2019 20:17

    bebatut on gh-pages

    Update on: Thu Jan 31 20:17:17 … (compare)

  • Jan 31 2019 19:44

    erasche on master

    fix typos Merge pull request #1236 from g… (compare)

  • Jan 31 2019 19:44
    erasche closed #1236
  • Jan 31 2019 19:44
    martenson opened #1236
  • Jan 31 2019 19:44

    martenson on martenson-patch-2

    fix typos (compare)

  • Jan 31 2019 19:23

    bebatut on gh-pages

    Update on: Thu Jan 31 19:23:39 … (compare)

  • Jan 31 2019 19:06

    Slugger70 on master

    import some notes fix username and 1 more (compare)

  • Jan 31 2019 19:06
    Slugger70 closed #1234
  • Jan 31 2019 19:04
    erasche review_requested #1234
  • Jan 31 2019 19:03
    erasche synchronize #1234
  • Jan 31 2019 19:03
    erasche unlabeled #1234
Tomas
@TKlingstrom
@shiltemann, thank you but how do I open it after starting the job? It's running as a job (ie yellow) but I find no way to boten it.
Saskia Hiltemann
@shiltemann
@TKlingstrom, in the "User" menu (top bar), go to "Active interactive tools"
@lldelisle oops, maybe one of the EU admins has an idea? @bgruening @gmauro?
Helena Rasche
@hexylena
I think the jenkins job which populates the library has not yet run?
but I don't know why there would be an empty folder there, if the shared-data hasn't run yet
very odd
Björn Grüning
@bgruening
trying to find the logs, but realistically I only have time this evening
Gianmauro Cuccuru
@gmauro
We have some issues with the Jenkins workers
I am working on that now
Björn Grüning
@bgruening
ConnectionError: Unexpected HTTP status code: 400: "Requested extension 'gz' unknown, cannot upload dataset."
Helena Rasche
@hexylena
but bjoern has it right
the extensions should be fastqsanger.gz
and bed
not .gz for all
Helena Rasche
@hexylena
yeah
Tomas
@TKlingstrom
@shiltemann yes that is how I've done it before but the notebook name is not clickable https://usegalaxy.eu/u/tomas/h/imported-covid-19-mrca-analysis
Helena Rasche
@hexylena
@TKlingstrom no, you need to find it under "User -> active interactive tools"
yes it makes no sense, yes we've complained, no, it still works like this a year later
Tomas
@TKlingstrom
But that is where I am clicking
Helena Rasche
@hexylena
ah? you should see an environment, it looks like it is running in the history you shared
Saskia Hiltemann
@shiltemann
@bgruening thanks for checking! guess we should update planemo, and adding some linting would probably also be good.
Tomas
@TKlingstrom
I uploaded a screenshot of the situation in the history I just shared
Saskia Hiltemann
@shiltemann
@lldelisle are you teaching this soon?
Helena Rasche
@hexylena
oh
unexpected place for a screenshot
Tomas
@TKlingstrom
picture
Helena Rasche
@hexylena
one sec
it's slow? cool :)
Tomas
@TKlingstrom
That was a bad way to phrase it
Helena Rasche
@hexylena
sometimes it takes a while for it to start
Tomas
@TKlingstrom
I can have a published history where I put screenshots, that worked
The notebook is not working.
Helena Rasche
@hexylena
ahh
Tomas
@TKlingstrom
Sorry
Helena Rasche
@hexylena
so the container is running, since 20 minutes. The script that writes the ports/etc to a .json file I guess didn't work. Out of my expertise lately, over to you @gmauro :)
galaxy@sn04:~$ gxadmin galaxy ie-show 8576421
Galaxy ID: 8576421
Condor ID: 3869527
Container: jupyter_notebook
Running on: vgcnbwc-interactive-c20me-0639.novalocal
Job script: /data/7/galaxy_db/pbs/galaxy_8576421.sh
Working dir: /data/dnb02/galaxy_db/job_working_directory/008/576/8576421
Container name: a97df9234f8e4568a6d4c91267bc96b1
Runtime:
cat: /data/dnb02/galaxy_db/job_working_directory/008/576/8576421/container_runtime.json: No such file or directory
sorry to not be more helpful
Tomas
@TKlingstrom
Well I am reassured that it is an actual error and not me being dense and that is helpful =).
Saskia Hiltemann
@shiltemann
@lldelisle this PR should hopefully fix it: galaxyproject/training-material#1909
Helena Rasche
@hexylena
@TKlingstrom you might try starting the container 2-3 more times, maybe you get lucky, and can kill the rest :)
Tomas
@TKlingstrom
I'll work on Ansible instead =).
Gianmauro Cuccuru
@gmauro
@TKlingstrom I am finishing a task, I can check it later.
Lucille Delisle
@lldelisle
Many thanks @shiltemann
Tomas
@TKlingstrom
@gmauro, thanks and no urgency at all from my side. I am experimenting to make sure things work smoothly for a discussion next week.
Helena Rasche
@hexylena
I've re-triggered the job @lldelisle, it will run whenever Gianmauro is finished with the jenkins workers, then the data libraries will be updated
Lucille Delisle
@lldelisle
@hexylena thank you very much
Gianmauro Cuccuru
@gmauro
@hexylena @lldelisle Jenkins is updating the data libraries